A virus lurking in deep space infects the crew of an earth shuttle on its way to Titan. The infected humans kill the crew they are supposed to be relieving, except for one man, Lowe, whom they infect. They begin preparing the base for breeding. Meanwhile, the TARDIS has been invaded by the same virus, and the Doctor becomes the host for the Nucleus of the Swarm. After he attempts to kill "The Reject" Leela (who is immune), the Doctor realizes what's happening and puts himself into a self-induced coma to keep from being taken over completely. Leela, accompanied by Lowe, rushes him to the Bi-Al Foundation hospital asteroid using the TARDIS, where she hopes Professor Marius will be able to find a cure.

Professor Marius, a kind old genius, immediately realises what's been going on. While Leela goes off to fight her attackers with the help of Marius' robot dog, K-9, the (still rapidly dying) Doctor asks Marius to make temporary clones of him and Leela. Lowe infects as many of the hospital staff as possible, and the cloned Doctor and Leela are shrunk down for a "Fantastic Voyage" Plot to try and destroy the virus by attacking it inside the Doctor's brain.

The short-lifespan clones expire before they can defeat the virus, but they drive the Nucleus out of the Doctor's brain, where it is expanded to human size. Lowe takes it back to Titan, to begin the breeding of a new giant shrimp virus super race, while Leela's decomposing clone corpse inside his brain gives the Doctor immunity to the virus. With the help of Professor Marius and K-9, the Doctor is able to isolate the immunity and synthesize a cure.

While Professor Marius treats the infected hospital staff, the travellers take the weaponized cure (and K-9) and head to Titan to finish off the virus. Leela knifes some people in the neck and keeps suggesting that the Doctor should just blow up the entire moon. He gives a grand spiel of not wanting to kill anyone, but eventually relents and blows up Titan. Professor Marius returns to Earth and gives K-9 to the Doctor as a souvenir.

Tropes:

Affably Evil: The Nucleus holds no particular grudge against the Doctor, and admits that the Doctor would be perfectly within his rights to kill him... if he can.

Artistic Licence Biology: The cloned Doctor and Leela spend ten minutes meandering around in the Doctor's brain. It looks like a giant cave system full of dangly bits.

Cloning Blues: The Virus seems to try to induce this in the Clone Doctor, but he doesn't mind dying to save his own life.

Detect Evil: Leela can "sense" the evil of the coming episode so strongly that she chews on the Doctor's scarf for comfort and forcibly prevents the Doctor from opening the TARDIS doors. Naturally, he ignores her.

Eternal English: Given the somewhat wobbly translation conventions of Doctor Who, this is always hard to say anything at all about. The exit sign on Titan clearly marked "EGGSIT", though, clearly suggests that they are using some version of English under a spelling reform in the 51st century.

Repeated at the hospital (the Doctor is placed in the "ISOLAYSHUN" ward, among other things).

Foreshadowing: At the very beginning of the episode, the Doctor compares humanity's explosion into the galaxy to a virus.

Genetic Memory: The clones of the Doctor and Leela have the memories of their originals. K9 explains that this is because they are more like "biological photocopies" than proper clones, hence their shortened lifespans. Which does not in any satisfactory way explain how they cloned their clothes. Homaged much later on in "The Doctor's Daughter".

Seeker White Blood Cells: While inside the Doctor's bodynote Yes, the Doctor travels inside his own body. It Makes Sense in Context., the Doctor and Leela are attacked by white blood cells, but the Doctor uses a nearby nerve cluster to send them a fake message summoning them to a different part of the body. Now, this wouldn't work in a human body, where white blood cells just wander aimlessly and deal with whatever they happen to come across, but maybe a Time Lord's immune system works differently.

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